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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG

Basic information

species Glycine max
transcript GLYMA18G17240.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g13720.1 (Oryza sativa), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttct---taaatt---tgtgtttagattttaggaatgattcttttattctctgttatat-tacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                          || |||||  |   || |||   ||    ||     ||| ||  |   |  |  |||  |  ||   |  || |  ||||| |||| |     | ||||  ||||||| ||||||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||  | ||||| ||| | ||  ||||||||
-------------------------gctcatattgttcgatagattcagtgccgctaatcagtagaaaacacaatcctgctcttggagatgcatgtaact--tttctatatcctctcggtgttgt--agATTCTTGAGATGGACACCTACAGATACCACGGACACTCTATGTCAGATCCAGGGAGCACTTACCGCACCAGAGATGAAATTGCAGGCATAAGACAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g50620.1 (Oryza sativa), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttctta--aatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                        |  || |   |  ||  | |||||    |         |||||    |||    | |  ||  | |   ||  |     |  |  | |  || | |  || |||| || ||||| || ||||| ||||||||||| || ||||| ||||| || ||||| ||||||||  | |||||||| || ||||||||||||
------------------------tggttgtgcctgctagcagtttgtagcaattcacccttaatgaaatgtttcagttttagtaagtgatggttactaatgtttccccactctttgtatttagGTTCTTGAAATGGATACCTACAGGTACCATGGCCATTCTATGTCAGATCCCGGAAGCACTTACCGTACCAGGGATGAGATCTCAGGTGTAAGACAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G361693_T01 (Zea mays), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattt---tgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                       | |    |  | | |  |  || |   ||  |    | || ||| ||| ||| |||  |     | ||| | |      | | |||   | |   | || || | || |||||||| || |||||||||||||||||||| ||||| ||||| || ||||| ||||| ||  | ||||||||||| ||||| || |||
---------------------aggcaagccttctccctgcaaatgcggagaggctc---gcataattatttcatt-tctagtgctgaagaatggttactaaaaccctaaggttctatatatctagGTCCTTGAGATGGATACCTACAGATACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G140150_T01 (Zea mays), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattc--tctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                   |  |        | || || | ||||| | | | ||      || ||| ||| |||   | || |  || |   || | |   |  || |  |   | | || || | || |||||||| || ||||| |||||||||||||| ||||| ||||| || ||||| ||||| ||  | ||||||||||| ||||| || |||
------------------gtgataagtgataacttgttcactttgtttgttggttc-----ataattatttaatttcatgtgctgaataatggtt-actaaaccctcatgttctatgtatctagGTCCTTGAGATGGATACCTACAGGTACCATGGCCACTCTATGTCAGATCCAGGAAGCACTTACCGCACCAGGGATGAGATTTCAGGTGTCAGGCAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G027627_T01 (Zea mays), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                          |||| | |     |   |     | | ||||  || |      ||| ||||     ||  |       |    |||||     |||| ||   ||||| || ||||||||||| ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||| | ||||||||  ||||  |||| |||
--------------------aggacccttaaactagacgaggcttgacatcggttttgtgattccagactttcttcttaaagatgctgatcaccacggttctattcgttttatgtt--tcagATCCTTGAGATGGACACCTACAGATACCACGGGCACTCAATGTCAGATCCAGGTAGCACCTACCGCACAAGGGATGAGATCGCTGGCATAAGGCAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G24180.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                   || || | | |      |    ||    ||||   | |    || || | ||   |  ||  |  ||||  |   |  |  | ||    ||||||| |  ||||| || ||||||||||| ||||||||||| || ||||| |||||||| || || ||||| |||||||| |||||||| || ||||| || ||||||
-------------------ttgtgaattcaatcacatagcgttgacatttatcgtatttttataatccattctctacctagtg-attatgaccaacata-ccattgccattattt-gcgcagATCCTTGAGATGGACACTTACAGATACCACGGTCACTCTATGTCTGACCCAGGAAGCACTTACCGTACTCGTGATGAAATCTCTGGCGTGAGACAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G59900.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                      | ||  ||      ||   ||    ||||  ||   |   | |||||||  |    | |   ||||||       |   ||  |   || || | | |||||||| ||||||||||||||||| ||||| || |||||||||||||||||||| |||||||||||||| || |||||||| |||||||| || |||
--------------------catataagtagtagctttggtttccaatttattttcctgtgtttattctttcctatcatat-ggattacaga-agcattaatacatcgtttcttctatacagATTCTTGAGATGGACACATACAGGTACCACGGTCACTCCATGTCTGATCCTGGGAGCACATACCGTACCCGAGATGAGATATCTGGTGTGAGGCAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0026g00990.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                   |||  |  |  |  |  | |  | | | ||| |   ||   |    ||  | |    |    || ||| |  || |||| ||| ||| |||  |  ||| |||||||| || |||||||| || || |||||||| |||||||||||||||||||| ||||| ||||||||||||||||||||||||||||| ||||||
------------------ctttaatgttgttgctagtaatttctctcttttggcattgtcatcattttatgtgagattgacta-attgc--tttatttttct-tctaaatgctggtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGCACCTACCGTACACGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g01940.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtaaatttacttcttttttgtacttatatttcttaaatttgtgtttagattttaggaatgattcttttattctctgttatattac-aattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                          | |  | |||||  |||  |   | ||   |     | ||  |||||       ||   | |   ||| || | ||| ||| |||  || ||| |||||||| || |||||||| || || |||||||| |||||||||||||||||||| || ||||||||||| |||||||||||||||||||| ||||||
----------------------cccgcctgcaattctttcattctttgcttgagcatgtctgtcatcattttacatgagattgactaattgatttatctttct-tctaaatgcttgtgttcagATTCTTGAAATGGACACTTATAGGTACCATGGTCACTCCATGTCTGATCCTGGGAGTACATACCGTACGCGTGATGAGATTTCTGGTGTGAGACAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S201_84V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------gtaagtaaatttacttcttttttgtacttata---tttcttaaatttg-tgt---ttagattttaggaatgattcttttattctctgttatattacaattgatttctctatcttaattattttgtcc-------agATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                            | |  |  ||    | | || || || | ||    |||  |  ||||| |||   ||  |  ||        || | |  |   |       ||    |||  |||| | ||| |||||| || ||        || || | |||||||| || |||||||| ||||| ||||| |||||||| || |||||||| ||||| || ||||||||||| ||||||||| |||||
gtaagtgatgctgttgttttcctaaccagcacatggatactttaccttcttctaatcatggggtttactccatttgctgtgtgttgcagctttacgtcagttatgtcgtaaccgagatgcttttgcttgggttctttttctgaattatattttctggcatggagGTTTTGGAGATGGATACGTACAGATATCATGGTCACTCTATGTCTGACCCAGGCAGCACCTACCGAACCCGTGATGAGATCTCTGGTGTACGACAG

upper sequence: GLYMA18G17240.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S47_1V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------gtaagtaaatttacttcttttttgtacttat-atttcttaaatttgtgtttagattttaggaatgattcttttattc-tctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                                       | |   |      |   |||   | ||||  |||  ||   | | |  | |  || ||    || |  | | |    |||  | | ||    ||  ||  |||    | |||  |   |  || |  | |||||||||||||| || || ||||| || |||||||| || || |||||||| ||||| || ||||| ||||| ||||||||  | || 
gtgtgtttacacgacgctcaacttctaagagaacacatctgaaagagcccgttcaatttgcttccttaggattgtttccgtatttactcacgttgtaattttgttgttgtgagcaatctactttgttttccttttttgttctgaacttatttctggatgaagGTCTTGGAGATGGACACATATAGGTATCATGGACATTCCATGTCCGACCCAGGCAGCACTTACCGAACTCGTGACGAGATCTCTGGTGTTCGTCAA

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|13480008|gb|BG509351.1|BG509351
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATT                         ATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|298196684|gb|HO041427.1|HO041427
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATT                         ATTCTCGAGATGGACACATACATATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|254334329|gb|GR844114.1|GR844114
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATT                         ATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|19937096|gb|BQ081145.1|BQ081145
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATT                         ATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
EST: gi|254322978|gb|GR835693.1|GR835693
EST:     AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATT                         ATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT
genomic: AACAAGCTTGTAAATTTGCAAAGGAGTTTGCTTTAAAGAATGGTCCCATTgtaagtaaat ... ttttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttattctctgttatattacaattgatttctctatcttaattattttgtccagATTCTCGAGATGGACACATACAGATACCATGGCCACTCCATGTCTGATCCTGGCAGCACATACCGTACACGTGATGAGATTTCTGGTGTAAGACAG
                                    tcttaat  putative branch site (score: 3)
                                             ttttgtcc  putative PPT
             ttatattacaattgat  TA-rich tract